chr13-111569284-C-T

Variant names:

• chr13-111569284-C-T
• rs1163623

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.85 in 152,242 control chromosomes in the GnomAD database, including 55,403 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.85 (55403 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.850 AC: 129348 AN: 152124 Hom.: 55376 Cov.: 33

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.883

Gnomad AMR AF: 0.901

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.935

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.863

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.850 AC: 129429 AN: 152242 Hom.: 55403 Cov.: 33 AF XY: 0.856 AC XY: 63721 AN XY: 74428

Gnomad4 AFR AF: 0.749

Gnomad4 AMR AF: 0.901

Gnomad4 ASJ AF: 0.880

Gnomad4 EAS AF: 0.965

Gnomad4 SAS AF: 0.915

Gnomad4 FIN AF: 0.935

Gnomad4 NFE AF: 0.871

Gnomad4 OTH AF: 0.862

Alfa AF: 0.858 Hom.: 9755

Bravo AF: 0.843

Asia WGS AF: 0.918 AC: 3193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.6
DANN	Benign	0.72

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1163623; hg19: chr13-112221631;